diff --git a/scripts/functions/logoP_snp.R b/scripts/functions/logoP_snp.R index b83ac0d..1ec6a68 100644 --- a/scripts/functions/logoP_snp.R +++ b/scripts/functions/logoP_snp.R @@ -272,11 +272,15 @@ LogoPlotSnps <- function(plot_df , limits = factor(1:length(x_axis_colname))) + theme(text = element_text(family="FreeSans") , legend.position = "none" - , axis.text.x = element_blank() - , axis.text.y = element_blank() + #, axis.text.x = element_blank() + #, axis.text.y = element_blank() #, axis.text.y = element_text() , axis.title.x = element_blank() - , axis.title.y = element_blank() + #, axis.title.y = element_blank() + , axis.title.y = element_text(size = y_tts + , angle = 90 + , colour = ytt_col + , margin = margin(t = 0, r = 0, b = 20, l = 0)) , plot.background = element_rect(fill = theme_bgc, colour=NA) ) + labs(x=NULL, y="WT") diff --git a/scripts/plotting/plotting_thesis/thesis-figs-alr.R b/scripts/plotting/plotting_thesis/thesis-figs-alr.R index 524f3e0..7d41218 100644 --- a/scripts/plotting/plotting_thesis/thesis-figs-alr.R +++ b/scripts/plotting/plotting_thesis/thesis-figs-alr.R @@ -73,20 +73,17 @@ tile_colour_map = c("DCS" = "#00ff00" ,"PLP" = "#000080") tile_legend=get_legend( - ggplot(tile_map, aes(factor(tile),y=0 , colour=tile_colour , fill=tile_colour))+ geom_tile() + - theme(legend.title = element_blank(), - legend.direction="horizontal", - legend.text = element_text(size=10), - legend.key.size = unit(10, "pt")) + - scale_colour_manual(name=NULL - #, values = tile_map$tile_colour + theme( + legend.direction="horizontal", + legend.text = element_text(size=10), + legend.key.size = unit(10, "pt")) + + scale_colour_manual(name="Active Site" , values=tile_colour_map) + - scale_fill_manual(name=NULL - #,values=tile_map$tile_colour + scale_fill_manual(name="Active Site" , values = tile_colour_map) ) @@ -198,7 +195,7 @@ logo_or_low = LogoPlotCustomH( lig3_colour = tile_map$tile_colour[4] ) -stability_low = stab() +stability_low = stab()+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3) # MID @@ -254,7 +251,7 @@ logo_p_snps_high = LogoPlotSnps( lig1_colour = tile_map$tile_colour[2], lig2_colour = tile_map$tile_colour[3], lig3_colour = tile_map$tile_colour[4] -) +)+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3) logo_or_high = LogoPlotCustomH( small_df3, @@ -270,10 +267,10 @@ logo_or_high = LogoPlotCustomH( lig1_colour = tile_map$tile_colour[2], lig2_colour = tile_map$tile_colour[3], lig3_colour = tile_map$tile_colour[4] -) +)+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3) -stability_high = stab() +stability_high = stab()+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3) #### "sorted" stability plots #### # do stability plots for later assembly @@ -297,7 +294,7 @@ stability_high_reorder = bp_stability_hmap( lig2_colour = tile_map$tile_colour[3], lig3_colour = tile_map$tile_colour[4] -) +)+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3) stability_centre_reorder = bp_stability_hmap( snpcount_low_high_df, reorder_position = T, diff --git a/scripts/plotting/plotting_thesis/thesis-figs-embb.R b/scripts/plotting/plotting_thesis/thesis-figs-embb.R index 9549d66..4d8d33e 100644 --- a/scripts/plotting/plotting_thesis/thesis-figs-embb.R +++ b/scripts/plotting/plotting_thesis/thesis-figs-embb.R @@ -7,8 +7,9 @@ # mutable_df3 = cbind(small_df3) # plot_df = cbind(small_df3) -source("~/git/LSHTM_analysis/config/embb.R") -source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R") +#source("~/git/LSHTM_analysis/config/embb.R") +#source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R") + #outdir="/home/pub/Work/LSHTM/Thesis_Plots/" outdir="~/git/Writing/thesis/tex/images-corrected/embb/" @@ -36,12 +37,11 @@ low_half_snpcount = round(nrow(snpcount_low_df)/2) snpcount_low_low_df = snpcount_low_df[1:low_half_snpcount,] snpcount_low_high_df = snpcount_low_df[low_half_snpcount:nrow(snpcount_low_df),] - # do stability plots for later assembly stability_high = bp_stability_hmap(snpcount_high_df, reorder_position = T, p_title = NULL, - my_ylab = NULL, + my_ylab = "", yvar_colname = 'avg_stability_scaled', stability_colname = "avg_stability_scaled", stability_outcome_colname = "avg_stability_outcome", @@ -75,7 +75,7 @@ stability_low = bp_stability_hmap(snpcount_low_low_df, yvar_colname = 'avg_stability_scaled', stability_colname = "avg_stability_scaled", stability_outcome_colname = "avg_stability_outcome", - my_ylab = NULL, + my_ylab = "", y_max_override = max(snpcount_high_df$pos_count), my_xaxls = 6, # x-axis label size my_yaxls = 8, # y-axis label size @@ -84,7 +84,7 @@ stability_low = bp_stability_hmap(snpcount_low_low_df, aa_pos_lig1=aa_pos_lig1, aa_pos_lig2=aa_pos_lig2, aa_pos_lig3=aa_pos_lig3 -) +)+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3) low=round(max(merged_df3$position)/3) centre=low*2 @@ -93,18 +93,18 @@ centre=low*2 heatbar_df = generate_distance_colour_map(merged_df3) heat_bar_legend = get_legend( - ggplot(merged_df3, aes(factor(ligand_distance), y=0)) + - theme(legend.direction="horizontal", - legend.title = element_text(size=10), - #legend.text = element_text(size=10), - #legend.key.size = unit(10, "pt") - )+ - geom_point(aes( - colour = ligand_distance, - - ) - ) + - scale_colour_gradientn(name="Ligand\nDistance (Å)", colours = magma(5, direction = -1)) + ggplot(merged_df3, aes(factor(ligand_distance), y=0)) + + theme(legend.direction="horizontal", + legend.title = element_text(size=10), + #legend.text = element_text(size=10), + #legend.key.size = unit(10, "pt") + )+ + geom_point(aes( + colour = ligand_distance, + + ) + ) + + scale_colour_gradientn(name="Ligand\nDistance (Å)", colours = magma(5, direction = -1)) ) # Position Tile Legend @@ -114,21 +114,18 @@ tile_colour_map = c("EMB" = "green" , "Ca" = "purple") tile_legend=get_legend( - - ggplot(tile_map, aes(factor(tile),y=0 - , colour=tile_colour - , fill=tile_colour))+ - geom_tile() + - theme(legend.title = element_blank(), - legend.direction="horizontal", - legend.text = element_text(size=10), - legend.key.size = unit(10, "pt")) + - scale_colour_manual(name=NULL - #, values = tile_map$tile_colour - , values=tile_colour_map) + - scale_fill_manual(name=NULL - #,values=tile_map$tile_colour - , values = tile_colour_map) + ggplot(tile_map, aes(factor(tile),y=0 + , colour=tile_colour + , fill=tile_colour))+ + geom_tile() + + theme( + legend.direction="horizontal", + legend.text = element_text(size=10), + legend.key.size = unit(10, "pt")) + + scale_colour_manual(name="Active Site" + , values=tile_colour_map) + + scale_fill_manual(name="Active Site" + , values = tile_colour_map) ) # SAV Tile Red/Blue Legend @@ -136,38 +133,39 @@ tile_legend=get_legend( temp_snp_df=merged_df3%>%dplyr::add_count(position) snp_tile_legend = get_legend( - ggplot(temp_snp_df, aes(factor(avg_stability_scaled), y=0)) + - theme(#legend.title = element_blank(), - legend.direction="horizontal", - legend.title = element_text(size=10), - #legend.text = element_text(size=10), - #legend.key.size = unit(10, "pt") - )+ - geom_point(aes( - colour = avg_stability_scaled, - - ) - ) + - scale_colour_gradientn(name="Protein Stability\n(ΔΔG Kcal/mol)", colours = rev(c("#007ba4", # rev() because FUCK - "#00bfc4", - "#ffffff", - "#ffd9d0", - "#f8766d", - "#ae3121"))) + ggplot(temp_snp_df, aes(factor(avg_stability_scaled), y=0)) + + theme(#legend.title = element_blank(), + legend.direction="horizontal", + legend.title = element_text(size=10), + #legend.text = element_text(size=10), + #legend.key.size = unit(10, "pt") + )+ + geom_point(aes( + colour = avg_stability_scaled, + + ) + ) + + scale_colour_gradientn(name="Protein Stability\n(ΔΔG Kcal/mol)", colours = rev(c("#007ba4", # rev() because FUCK + "#00bfc4", + "#ffffff", + "#ffd9d0", + "#f8766d", + "#ae3121"))) ) # Logop Chemistry Colours temp_logo_p_snp=cbind(merged_df3) tab_mt = table(temp_logo_p_snp[["mutant_type"]], temp_logo_p_snp[["position"]]) tab_mt = unclass(tab_mt) logoplot_chemistry_legend=get_legend( - ggplot() + - geom_logo(tab_mt - , method = 'custom' - , col_scheme = "chemistry" - , seq_type = 'aa') + theme(legend.title = element_blank(), - legend.direction="horizontal", - legend.text = element_text(size=10), - legend.key.size = unit(10, "pt")) + ggplot() + + geom_logo(tab_mt + , method = 'custom' + , col_scheme = "chemistry" + , seq_type = 'aa') + theme( + legend.title = element_blank(), + legend.direction="horizontal", + legend.text = element_text(size=10), + legend.key.size = unit(10, "pt")) ) # LOW @@ -187,7 +185,7 @@ logo_p_snps_low = LogoPlotSnps(mutable_df3, # needs to be: active_aa_pos AND odds ratio >10 logo_or_low = LogoPlotCustomH(small_df3, y_axis_increment=10, - y_lab="", + y_lab="Odds Ratio", rm_empty_y=T, aa_pos_drug=aa_pos_drug, active_aa_pos=active_aa_pos, @@ -201,10 +199,21 @@ logo_or_low = LogoPlotCustomH(small_df3, small_df3 = merged_df3[merged_df3['position'] <= centre & merged_df3['position'] >= low,] mutable_df3 = cbind(small_df3) print(paste0("Plotting MID Rows: ", nrow(small_df3))) -logo_p_snps_centre = LogoPlotSnps(mutable_df3, y_lab = "SAV Count") + +logo_p_snps_centre = LogoPlotSnps( + mutable_df3, + aa_pos_drug=aa_pos_drug, + active_aa_pos=active_aa_pos, + aa_pos_lig1=aa_pos_lig1, + aa_pos_lig2=aa_pos_lig2, + aa_pos_lig3=aa_pos_lig3, + y_lab = "SAV Count" +) logo_or_centre = LogoPlotCustomH(small_df3, - y_axis_increment=10, + y_axis_increment=2, + y_lab = "Log(10) Odds Ratio", + y_axis_log = TRUE, rm_empty_y=T, aa_pos_drug=aa_pos_drug, active_aa_pos=active_aa_pos, @@ -221,47 +230,49 @@ print(paste0("Plotting HIGH Rows: ", nrow(small_df3))) logo_p_snps_high = LogoPlotSnps(mutable_df3, y_lab="", + x_lab = "Position", aa_pos_drug=aa_pos_drug, active_aa_pos=active_aa_pos, aa_pos_lig1=aa_pos_lig1, aa_pos_lig2=aa_pos_lig2, aa_pos_lig3=aa_pos_lig3 -) +) + annotate(geom="text", label="Position",x=0.5,y=0.025, size=3) + logo_or_high = LogoPlotCustomH(small_df3, y_axis_increment=10, - y_lab="", + y_lab="Odds Ratio", rm_empty_y=T, aa_pos_drug=aa_pos_drug, active_aa_pos=active_aa_pos, aa_pos_lig1=aa_pos_lig1, aa_pos_lig2=aa_pos_lig2, aa_pos_lig3=aa_pos_lig3 -) +)+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3) jpeg(paste0(outdir,"embb_average_stability.jpeg"), height = 8.25, width=11.5, unit="in",res=300) cowplot::plot_grid( - cowplot::plot_grid(heat_bar_legend, tile_legend, snp_tile_legend, nrow=1), - cowplot::plot_grid(stability_high, stability_centre, stability_low,ncol=1), - ncol=1, - rel_heights = c(1,12) + cowplot::plot_grid(heat_bar_legend, tile_legend, snp_tile_legend, nrow=1), + cowplot::plot_grid(stability_high, stability_centre, stability_low,ncol=1), + ncol=1, + rel_heights = c(1,12) ) dev.off() jpeg(paste0(outdir,"embb_snp.jpeg"), height = 8.25, width=11.5, unit="in",res=300) cowplot::plot_grid( - cowplot::plot_grid(heat_bar_legend, tile_legend, logoplot_chemistry_legend, nrow=1), - cowplot::plot_grid(logo_p_snps_low, logo_p_snps_centre, logo_p_snps_high, ncol=1, align='hv'), - ncol=1, - rel_heights = c(1,12) + cowplot::plot_grid(heat_bar_legend, tile_legend, logoplot_chemistry_legend, nrow=1), + cowplot::plot_grid(logo_p_snps_low, logo_p_snps_centre, logo_p_snps_high, ncol=1, align='hv'), + ncol=1, + rel_heights = c(1,12) ) dev.off() jpeg(paste0(outdir,"embb_or.jpeg"), height = 8.25, width=11.5, unit="in",res=300) cowplot::plot_grid( - cowplot::plot_grid(heat_bar_legend, tile_legend, logoplot_chemistry_legend, nrow=1), - cowplot::plot_grid(logo_or_low, logo_or_centre, logo_or_high, ncol=1, align='hv'), - ncol=1, - rel_heights = c(1,12) + cowplot::plot_grid(heat_bar_legend, tile_legend, logoplot_chemistry_legend, nrow=1), + cowplot::plot_grid(logo_or_low, logo_or_centre, logo_or_high, ncol=1, align='hv'), + ncol=1, + rel_heights = c(1,12) ) dev.off() diff --git a/scripts/plotting/plotting_thesis/thesis-figs-gid.R b/scripts/plotting/plotting_thesis/thesis-figs-gid.R index 0ed6751..428f35d 100644 --- a/scripts/plotting/plotting_thesis/thesis-figs-gid.R +++ b/scripts/plotting/plotting_thesis/thesis-figs-gid.R @@ -70,21 +70,18 @@ tile_colour_map = c("STR" = "green", ,"AMP" = "#000080") tile_legend=get_legend( - - ggplot(tile_map, aes(factor(tile),y=0 - , colour=tile_colour - , fill=tile_colour))+ - geom_tile() + - theme(legend.title = element_blank(), - legend.direction="horizontal", - legend.text = element_text(size=10), - legend.key.size = unit(10, "pt")) + - scale_colour_manual(name=NULL - #, values = tile_map$tile_colour - , values=tile_colour_map) + - scale_fill_manual(name=NULL - #,values=tile_map$tile_colour - , values = tile_colour_map) + ggplot(tile_map, aes(factor(tile),y=0 + , colour=tile_colour + , fill=tile_colour))+ + geom_tile() + + theme( + legend.direction="horizontal", + legend.text = element_text(size=10), + legend.key.size = unit(10, "pt")) + + scale_colour_manual(name="Active Site" + , values=tile_colour_map) + + scale_fill_manual(name="Active Site" + , values = tile_colour_map) ) # SAV Tile Red/Blue Legend @@ -271,7 +268,7 @@ logo_or_high = LogoPlotCustomH( ) -stability_high = stab() +stability_high = stab()+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3) #### "sorted" stability plots #### # do stability plots for later assembly diff --git a/scripts/plotting/plotting_thesis/thesis-figs-katg.R b/scripts/plotting/plotting_thesis/thesis-figs-katg.R index 2281b96..6e7cb1e 100644 --- a/scripts/plotting/plotting_thesis/thesis-figs-katg.R +++ b/scripts/plotting/plotting_thesis/thesis-figs-katg.R @@ -51,20 +51,20 @@ centre=low*2 heatbar_df = generate_distance_colour_map(merged_df3) heat_bar_legend = get_legend( - ggplot(merged_df3, aes(factor(ligand_distance), y=0)) + - theme(legend.direction="horizontal", - legend.title = element_text(size=10), - #legend.text = element_text(size=10), - #legend.key.size = unit(10, "pt") - )+ - geom_point(aes( - colour = ligand_distance, - - ) - ) + - scale_colour_gradientn( - name="Ligand\nDistance (Å)", - colours = magma(5, direction = -1)) + ggplot(merged_df3, aes(factor(ligand_distance), y=0)) + + theme(legend.direction="horizontal", + legend.title = element_text(size=10), + #legend.text = element_text(size=10), + #legend.key.size = unit(10, "pt") + )+ + geom_point(aes( + colour = ligand_distance, + + ) + ) + + scale_colour_gradientn( + name="Ligand\nDistance (Å)", + colours = magma(5, direction = -1)) ) # Position Tile Legend # STR #00ff00 @@ -72,21 +72,18 @@ tile_colour_map = c("INH" = "#00ff00" ,"HEME" = "darkslategrey") tile_legend=get_legend( - - ggplot(tile_map, aes(factor(tile),y=0 - , colour=tile_colour - , fill=tile_colour))+ - geom_tile() + - theme(legend.title = element_blank(), - legend.direction="horizontal", - legend.text = element_text(size=10), - legend.key.size = unit(10, "pt")) + - scale_colour_manual(name=NULL - #, values = tile_map$tile_colour - , values=tile_colour_map) + - scale_fill_manual(name=NULL - #,values=tile_map$tile_colour - , values = tile_colour_map) + ggplot(tile_map, aes(factor(tile),y=0 + , colour=tile_colour + , fill=tile_colour))+ + geom_tile() + + theme( + legend.direction="horizontal", + legend.text = element_text(size=10), + legend.key.size = unit(10, "pt")) + + scale_colour_manual(name="Active Site" + , values=tile_colour_map) + + scale_fill_manual(name="Active Site" + , values = tile_colour_map) ) # SAV Tile Red/Blue Legend @@ -94,67 +91,67 @@ tile_legend=get_legend( temp_snp_df=merged_df3%>%dplyr::add_count(position) snp_tile_legend = get_legend( - ggplot(temp_snp_df, aes(factor(avg_stability_scaled), y=0)) + - theme(#legend.title = element_blank(), - legend.direction="horizontal", - legend.title = element_text(size=10), - #legend.text = element_text(size=10), - #legend.key.size = unit(10, "pt") - )+ - geom_point(aes( - colour = avg_stability_scaled, - - ) - ) + - scale_colour_gradientn( - name="Protein Stability\n(ΔΔG Kcal/mol)", colours = rev( - c("#007ba4", # rev() because FUCK - "#00bfc4", - "#ffffff", - "#ffd9d0", - "#f8766d", - "#ae3121") - ) - ) + ggplot(temp_snp_df, aes(factor(avg_stability_scaled), y=0)) + + theme(#legend.title = element_blank(), + legend.direction="horizontal", + legend.title = element_text(size=10), + #legend.text = element_text(size=10), + #legend.key.size = unit(10, "pt") + )+ + geom_point(aes( + colour = avg_stability_scaled, + + ) + ) + + scale_colour_gradientn( + name="Protein Stability\n(ΔΔG Kcal/mol)", colours = rev( + c("#007ba4", # rev() because FUCK + "#00bfc4", + "#ffffff", + "#ffd9d0", + "#f8766d", + "#ae3121") + ) + ) ) # Logop Chemistry Colours temp_logo_p_snp=cbind(merged_df3) tab_mt = table(temp_logo_p_snp[["mutant_type"]], temp_logo_p_snp[["position"]]) tab_mt = unclass(tab_mt) logoplot_chemistry_legend=get_legend( - ggplot() + - geom_logo( - tab_mt - , method = 'custom' - , col_scheme = "chemistry" - , seq_type = 'aa') + theme( - legend.title = element_blank(), - legend.direction="horizontal", - legend.text = element_text(size=10), - legend.key.size = unit(10, "pt") - ) + ggplot() + + geom_logo( + tab_mt + , method = 'custom' + , col_scheme = "chemistry" + , seq_type = 'aa') + theme( + legend.title = element_blank(), + legend.direction="horizontal", + legend.text = element_text(size=10), + legend.key.size = unit(10, "pt") + ) ) stab=function(...){bp_stability_hmap( - small_df3, - p_title = NULL, - yvar_colname = 'avg_stability_scaled', - stability_colname = "avg_stability_scaled", - stability_outcome_colname = "avg_stability_outcome", - my_ylab = "", - my_xaxls = 6, # x-axis label size - my_yaxls = 8, # y-axis label size - drug_colour = tile_map$tile_colour[1], - lig1_colour = tile_map$tile_colour[2], - lig2_colour = tile_map$tile_colour[3], - lig3_colour = tile_map$tile_colour[4], - aa_pos_drug=aa_pos_drug, - active_aa_pos=active_aa_pos, - aa_pos_lig1=aa_pos_lig1, - aa_pos_lig2=aa_pos_lig2, - aa_pos_lig3=aa_pos_lig3, - y_max_override=max(merged_df3$pos_count), - ... + small_df3, + p_title = NULL, + yvar_colname = 'avg_stability_scaled', + stability_colname = "avg_stability_scaled", + stability_outcome_colname = "avg_stability_outcome", + my_ylab = "", + my_xaxls = 6, # x-axis label size + my_yaxls = 8, # y-axis label size + drug_colour = tile_map$tile_colour[1], + lig1_colour = tile_map$tile_colour[2], + lig2_colour = tile_map$tile_colour[3], + lig3_colour = tile_map$tile_colour[4], + aa_pos_drug=aa_pos_drug, + active_aa_pos=active_aa_pos, + aa_pos_lig1=aa_pos_lig1, + aa_pos_lig2=aa_pos_lig2, + aa_pos_lig3=aa_pos_lig3, + y_max_override=max(merged_df3$pos_count), + ... ) } @@ -167,38 +164,38 @@ print(paste0("Plotting LOW Rows: ", nrow(small_df3))) logo_p_snps_low = LogoPlotSnps( - mutable_df3, - y_lab="", - aa_pos_drug=aa_pos_drug, - active_aa_pos=active_aa_pos, - aa_pos_lig1=aa_pos_lig1, - aa_pos_lig2=aa_pos_lig2, - aa_pos_lig3=aa_pos_lig3, - drug_colour = tile_map$tile_colour[1], - lig1_colour = tile_map$tile_colour[2], - lig2_colour = tile_map$tile_colour[3], - lig3_colour = tile_map$tile_colour[4] + mutable_df3, + y_lab="", + aa_pos_drug=aa_pos_drug, + active_aa_pos=active_aa_pos, + aa_pos_lig1=aa_pos_lig1, + aa_pos_lig2=aa_pos_lig2, + aa_pos_lig3=aa_pos_lig3, + drug_colour = tile_map$tile_colour[1], + lig1_colour = tile_map$tile_colour[2], + lig2_colour = tile_map$tile_colour[3], + lig3_colour = tile_map$tile_colour[4] ) # needs to be: active_aa_pos AND odds ratio >10 logo_or_low = LogoPlotCustomH( - small_df3, - y_lab = "Odds Ratio", - # y_axis_increment=1, - # y_axis_log = TRUE, - rm_empty_y=TRUE, - aa_pos_drug=aa_pos_drug, - active_aa_pos=active_aa_pos, - aa_pos_lig1=aa_pos_lig1, - aa_pos_lig2=aa_pos_lig2, - aa_pos_lig3=aa_pos_lig3, - drug_colour = tile_map$tile_colour[1], - lig1_colour = tile_map$tile_colour[2], - lig2_colour = tile_map$tile_colour[3], - lig3_colour = tile_map$tile_colour[4] + small_df3, + y_lab = "Odds Ratio", + # y_axis_increment=1, + # y_axis_log = TRUE, + rm_empty_y=TRUE, + aa_pos_drug=aa_pos_drug, + active_aa_pos=active_aa_pos, + aa_pos_lig1=aa_pos_lig1, + aa_pos_lig2=aa_pos_lig2, + aa_pos_lig3=aa_pos_lig3, + drug_colour = tile_map$tile_colour[1], + lig1_colour = tile_map$tile_colour[2], + lig2_colour = tile_map$tile_colour[3], + lig3_colour = tile_map$tile_colour[4] ) -stability_low = stab() +stability_low = stab()+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3) # MID @@ -207,34 +204,34 @@ mutable_df3 = cbind(small_df3) print(paste0("Plotting MID Rows: ", nrow(small_df3))) logo_p_snps_centre = LogoPlotSnps( - mutable_df3, - y_lab = "", - aa_pos_drug=aa_pos_drug, - active_aa_pos=active_aa_pos, - aa_pos_lig1=aa_pos_lig1, - aa_pos_lig2=aa_pos_lig2, - aa_pos_lig3=aa_pos_lig3, - drug_colour = tile_map$tile_colour[1], - lig1_colour = tile_map$tile_colour[2], - lig2_colour = tile_map$tile_colour[3], - lig3_colour = tile_map$tile_colour[4] + mutable_df3, + y_lab = "", + aa_pos_drug=aa_pos_drug, + active_aa_pos=active_aa_pos, + aa_pos_lig1=aa_pos_lig1, + aa_pos_lig2=aa_pos_lig2, + aa_pos_lig3=aa_pos_lig3, + drug_colour = tile_map$tile_colour[1], + lig1_colour = tile_map$tile_colour[2], + lig2_colour = tile_map$tile_colour[3], + lig3_colour = tile_map$tile_colour[4] ) logo_or_centre = LogoPlotCustomH( - small_df3, - y_axis_increment=2, - rm_empty_y=TRUE, - y_lab = "Log(10) Odds Ratio", - y_axis_log = TRUE, - aa_pos_drug=aa_pos_drug, - active_aa_pos=active_aa_pos, - aa_pos_lig1=aa_pos_lig1, - aa_pos_lig2=aa_pos_lig2, - aa_pos_lig3=aa_pos_lig3, - drug_colour = tile_map$tile_colour[1], - lig1_colour = tile_map$tile_colour[2], - lig2_colour = tile_map$tile_colour[3], - lig3_colour = tile_map$tile_colour[4] + small_df3, + y_axis_increment=2, + rm_empty_y=TRUE, + y_lab = "Log(10) Odds Ratio", + y_axis_log = TRUE, + aa_pos_drug=aa_pos_drug, + active_aa_pos=active_aa_pos, + aa_pos_lig1=aa_pos_lig1, + aa_pos_lig2=aa_pos_lig2, + aa_pos_lig3=aa_pos_lig3, + drug_colour = tile_map$tile_colour[1], + lig1_colour = tile_map$tile_colour[2], + lig2_colour = tile_map$tile_colour[3], + lig3_colour = tile_map$tile_colour[4] ) stability_centre = stab() @@ -246,35 +243,35 @@ print(paste0("Plotting HIGH Rows: ", nrow(small_df3))) logo_p_snps_high = LogoPlotSnps( - mutable_df3, - y_lab="" , - aa_pos_drug=aa_pos_drug, - active_aa_pos=active_aa_pos, - aa_pos_lig1=aa_pos_lig1, - aa_pos_lig2=aa_pos_lig2, - aa_pos_lig3=aa_pos_lig3, - drug_colour = tile_map$tile_colour[1], - lig1_colour = tile_map$tile_colour[2], - lig2_colour = tile_map$tile_colour[3], - lig3_colour = tile_map$tile_colour[4] -) + mutable_df3, + y_lab="" , + aa_pos_drug=aa_pos_drug, + active_aa_pos=active_aa_pos, + aa_pos_lig1=aa_pos_lig1, + aa_pos_lig2=aa_pos_lig2, + aa_pos_lig3=aa_pos_lig3, + drug_colour = tile_map$tile_colour[1], + lig1_colour = tile_map$tile_colour[2], + lig2_colour = tile_map$tile_colour[3], + lig3_colour = tile_map$tile_colour[4] +)+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3) logo_or_high = LogoPlotCustomH( - small_df3, - y_axis_increment=10, - rm_empty_y=TRUE, - # y_axis_log = TRUE, - y_lab = "Odds Ratio", - aa_pos_drug=aa_pos_drug, - active_aa_pos=active_aa_pos, - aa_pos_lig1=aa_pos_lig1, - aa_pos_lig2=aa_pos_lig2, - aa_pos_lig3=aa_pos_lig3, - drug_colour = tile_map$tile_colour[1], - lig1_colour = tile_map$tile_colour[2], - lig2_colour = tile_map$tile_colour[3], - lig3_colour = tile_map$tile_colour[4] -) + small_df3, + y_axis_increment=10, + rm_empty_y=TRUE, + # y_axis_log = TRUE, + y_lab = "Odds Ratio", + aa_pos_drug=aa_pos_drug, + active_aa_pos=active_aa_pos, + aa_pos_lig1=aa_pos_lig1, + aa_pos_lig2=aa_pos_lig2, + aa_pos_lig3=aa_pos_lig3, + drug_colour = tile_map$tile_colour[1], + lig1_colour = tile_map$tile_colour[2], + lig2_colour = tile_map$tile_colour[3], + lig3_colour = tile_map$tile_colour[4] +)+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3) stability_high = stab() @@ -282,103 +279,103 @@ stability_high = stab() # do stability plots for later assembly stability_high_reorder = bp_stability_hmap( - snpcount_high_df, - reorder_position = T, - p_title = NULL, - my_ylab = NULL, - yvar_colname = 'avg_stability_scaled', - stability_colname = "avg_stability_scaled", - stability_outcome_colname = "avg_stability_outcome", - my_xaxls = 4, # x-axis label size - my_yaxls = 8, # y-axis label size - aa_pos_drug=aa_pos_drug, - active_aa_pos=active_aa_pos, - aa_pos_lig1=aa_pos_lig1, - aa_pos_lig2=aa_pos_lig2, - aa_pos_lig3=aa_pos_lig3, - drug_colour = tile_map$tile_colour[1], - lig1_colour = tile_map$tile_colour[2], - lig2_colour = tile_map$tile_colour[3], - lig3_colour = tile_map$tile_colour[4] - -) + snpcount_high_df, + reorder_position = T, + p_title = NULL, + my_ylab = NULL, + yvar_colname = 'avg_stability_scaled', + stability_colname = "avg_stability_scaled", + stability_outcome_colname = "avg_stability_outcome", + my_xaxls = 4, # x-axis label size + my_yaxls = 8, # y-axis label size + aa_pos_drug=aa_pos_drug, + active_aa_pos=active_aa_pos, + aa_pos_lig1=aa_pos_lig1, + aa_pos_lig2=aa_pos_lig2, + aa_pos_lig3=aa_pos_lig3, + drug_colour = tile_map$tile_colour[1], + lig1_colour = tile_map$tile_colour[2], + lig2_colour = tile_map$tile_colour[3], + lig3_colour = tile_map$tile_colour[4] + +)+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3) stability_centre_reorder = bp_stability_hmap( - snpcount_low_high_df, - reorder_position = T, - p_title = NULL, - yvar_colname = 'avg_stability_scaled', - stability_colname = "avg_stability_scaled", - stability_outcome_colname = "avg_stability_outcome", - my_ylab = "", - y_max_override = max(snpcount_high_df$pos_count), - my_xaxls = 6, # x-axis label size - my_yaxls = 8, # y-axis label size - aa_pos_drug=aa_pos_drug, - active_aa_pos=active_aa_pos, - aa_pos_lig1=aa_pos_lig1, - aa_pos_lig2=aa_pos_lig2, - aa_pos_lig3=aa_pos_lig3, - drug_colour = tile_map$tile_colour[1], - lig1_colour = tile_map$tile_colour[2], - lig2_colour = tile_map$tile_colour[3], - lig3_colour = tile_map$tile_colour[4] + snpcount_low_high_df, + reorder_position = T, + p_title = NULL, + yvar_colname = 'avg_stability_scaled', + stability_colname = "avg_stability_scaled", + stability_outcome_colname = "avg_stability_outcome", + my_ylab = "", + y_max_override = max(snpcount_high_df$pos_count), + my_xaxls = 6, # x-axis label size + my_yaxls = 8, # y-axis label size + aa_pos_drug=aa_pos_drug, + active_aa_pos=active_aa_pos, + aa_pos_lig1=aa_pos_lig1, + aa_pos_lig2=aa_pos_lig2, + aa_pos_lig3=aa_pos_lig3, + drug_colour = tile_map$tile_colour[1], + lig1_colour = tile_map$tile_colour[2], + lig2_colour = tile_map$tile_colour[3], + lig3_colour = tile_map$tile_colour[4] ) stability_low_reorder = bp_stability_hmap( - snpcount_low_low_df, - reorder_position = T, - p_title = NULL, - yvar_colname = 'avg_stability_scaled', - stability_colname = "avg_stability_scaled", - stability_outcome_colname = "avg_stability_outcome", - my_ylab = NULL, - y_max_override = max(snpcount_high_df$pos_count), - my_xaxls = 6, # x-axis label size - my_yaxls = 8, # y-axis label size - aa_pos_drug=aa_pos_drug, - active_aa_pos=active_aa_pos, - aa_pos_lig1=aa_pos_lig1, - aa_pos_lig2=aa_pos_lig2, - aa_pos_lig3=aa_pos_lig3, - drug_colour = tile_map$tile_colour[1], - lig1_colour = tile_map$tile_colour[2], - lig2_colour = tile_map$tile_colour[3], - lig3_colour = tile_map$tile_colour[4] - + snpcount_low_low_df, + reorder_position = T, + p_title = NULL, + yvar_colname = 'avg_stability_scaled', + stability_colname = "avg_stability_scaled", + stability_outcome_colname = "avg_stability_outcome", + my_ylab = NULL, + y_max_override = max(snpcount_high_df$pos_count), + my_xaxls = 6, # x-axis label size + my_yaxls = 8, # y-axis label size + aa_pos_drug=aa_pos_drug, + active_aa_pos=active_aa_pos, + aa_pos_lig1=aa_pos_lig1, + aa_pos_lig2=aa_pos_lig2, + aa_pos_lig3=aa_pos_lig3, + drug_colour = tile_map$tile_colour[1], + lig1_colour = tile_map$tile_colour[2], + lig2_colour = tile_map$tile_colour[3], + lig3_colour = tile_map$tile_colour[4] + ) jpeg(paste0(outdir,"katg_average_stability-sorted.jpeg"), height = 6, width=11.5, unit="in",res=300) cowplot::plot_grid( - cowplot::plot_grid(heat_bar_legend, tile_legend, snp_tile_legend, nrow=1), - cowplot::plot_grid(stability_high_reorder, stability_centre_reorder, stability_low_reorder,ncol=1), - ncol=1, - rel_heights = c(1,12) + cowplot::plot_grid(heat_bar_legend, tile_legend, snp_tile_legend, nrow=1), + cowplot::plot_grid(stability_high_reorder, stability_centre_reorder, stability_low_reorder,ncol=1), + ncol=1, + rel_heights = c(1,12) ) dev.off() jpeg(paste0(outdir,"katg_average_stability-unsorted.jpeg"), height = 6, width=11.5, unit="in",res=300) cowplot::plot_grid( - cowplot::plot_grid(heat_bar_legend, tile_legend, snp_tile_legend, nrow=1), - cowplot::plot_grid(stability_high, stability_centre, stability_low,ncol=1), - ncol=1, - rel_heights = c(1,12) + cowplot::plot_grid(heat_bar_legend, tile_legend, snp_tile_legend, nrow=1), + cowplot::plot_grid(stability_high, stability_centre, stability_low,ncol=1), + ncol=1, + rel_heights = c(1,12) ) dev.off() jpeg(paste0(outdir,"katg_snp.jpeg"), height = 6, width=11.5, unit="in",res=300) cowplot::plot_grid( - cowplot::plot_grid(heat_bar_legend, tile_legend, logoplot_chemistry_legend, nrow=1), - cowplot::plot_grid(logo_p_snps_low, logo_p_snps_centre, logo_p_snps_high, ncol=1, align='hv'), - ncol=1, - rel_heights = c(1,12) + cowplot::plot_grid(heat_bar_legend, tile_legend, logoplot_chemistry_legend, nrow=1), + cowplot::plot_grid(logo_p_snps_low, logo_p_snps_centre, logo_p_snps_high, ncol=1, align='hv'), + ncol=1, + rel_heights = c(1,12) ) dev.off() jpeg(paste0(outdir,"katg_or.jpeg"), height = 6, width=11.5, unit="in",res=300) cowplot::plot_grid( - cowplot::plot_grid(heat_bar_legend, tile_legend, logoplot_chemistry_legend, nrow=1), - cowplot::plot_grid(logo_or_low, logo_or_centre, logo_or_high, ncol=1, align='hv'), - ncol=1, - rel_heights = c(1,12) + cowplot::plot_grid(heat_bar_legend, tile_legend, logoplot_chemistry_legend, nrow=1), + cowplot::plot_grid(logo_or_low, logo_or_centre, logo_or_high, ncol=1, align='hv'), + ncol=1, + rel_heights = c(1,12) ) dev.off() diff --git a/scripts/plotting/plotting_thesis/thesis-figs-rpob.R b/scripts/plotting/plotting_thesis/thesis-figs-rpob.R index e15c97f..2570c18 100644 --- a/scripts/plotting/plotting_thesis/thesis-figs-rpob.R +++ b/scripts/plotting/plotting_thesis/thesis-figs-rpob.R @@ -71,20 +71,17 @@ heat_bar_legend = get_legend( tile_colour_map = c("RFP" = "#00ff00") tile_legend=get_legend( - ggplot(tile_map, aes(factor(tile),y=0 , colour=tile_colour , fill=tile_colour))+ geom_tile() + - theme(legend.title = element_blank(), - legend.direction="horizontal", - legend.text = element_text(size=10), - legend.key.size = unit(10, "pt")) + - scale_colour_manual(name=NULL - #, values = tile_map$tile_colour + theme( + legend.direction="horizontal", + legend.text = element_text(size=10), + legend.key.size = unit(10, "pt")) + + scale_colour_manual(name="Active Site" , values=tile_colour_map) + - scale_fill_manual(name=NULL - #,values=tile_map$tile_colour + scale_fill_manual(name="Active Site" , values = tile_colour_map) ) @@ -260,7 +257,7 @@ logo_p_snps_high = LogoPlotSnps( lig1_colour = tile_map$tile_colour[2], lig2_colour = tile_map$tile_colour[3], lig3_colour = tile_map$tile_colour[4] -) +)+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3) logo_or_high = LogoPlotCustomH( small_df3, @@ -277,10 +274,10 @@ logo_or_high = LogoPlotCustomH( lig1_colour = tile_map$tile_colour[2], lig2_colour = tile_map$tile_colour[3], lig3_colour = tile_map$tile_colour[4] -) +)+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3) -stability_low = stab(my_xaxls = 4) +stability_low = stab(my_xaxls = 4)+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3) #### "sorted" stability plots #### # do stability plots for later assembly @@ -304,7 +301,7 @@ stability_high_reorder = bp_stability_hmap( lig2_colour = tile_map$tile_colour[3], lig3_colour = tile_map$tile_colour[4] -) +)+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3) stability_centre_reorder = bp_stability_hmap( snpcount_low_high_df, reorder_position = T, diff --git a/scripts/thesis_summary_table.R b/scripts/thesis_summary_table.R index 5a73592..1942e50 100644 --- a/scripts/thesis_summary_table.R +++ b/scripts/thesis_summary_table.R @@ -187,7 +187,7 @@ loaded_files$gid_baselineC_cd_sl[loaded_files$gid_baselineC_cd_sl$source_data==" for (x in gene) { out_tex=paste0(latex_outdir,"ml_table-", x, ".tex") df_name=paste0(x,"_baselineC_cd_sl") - processed_df = loaded_files[[df_name]] %>% pivot_wider(names_from=source_data, values_from=c( + processed_df = loaded_files[[df_name]] %>% pivotf_wider(names_from=source_data, values_from=c( 'MCC', 'F1', 'Accuracy',